Latest Generation DNA Sequencing System to Boost Animal Conservation Research

By BiotechDaily International staff writersPosted on 23 Feb 2012

A state-of-the-art DNA sequencing system will soon be applied to solving problems related to the conservation and maintenance of endangered animal species.

The Smithsonian Conservation Biology Institute (Washington DC, USA) has announced plans to collaborate with Roche (Basel, Switzerland) in order to apply the Roche GS Junior benchtop DNA sequencing system to research in the Smithsonian Conservation Biology Institute’s Center for Conservation and Evolutionary Genetics.

The GS Junior system will be housed in a state-of-the-art genetics laboratory at the [US] National Zoo in Washington DC. The DNA sequencing powers of the GS Junior system will be used for a variety of research projects in areas of animal disease resistance, population genetics, and molecular ecology.

The GS Junior System supports the sequencing of samples from a wide variety of starting materials including genomic DNA and PCR products. Samples such as genomic DNA are randomly fragmented into small, 300 to 800-basepair pieces. For smaller samples, such as small noncoding RNA or PCR amplicons, fragmentation is not required.

Using a series of standard molecular biology techniques, short DNA adaptors are added to each library fragment. These adaptors are then used in subsequent quantification, amplification, and sequencing steps. The single-stranded DNA library is immobilized onto specifically designed DNA capture beads. Each bead carries a unique single-stranded DNA library fragment. The bead-bound library is emulsified with amplification reagents in a water-in-oil mixture resulting in microreactors containing just one bead with one unique sample-library fragment.

Each unique sample library fragment is clonally amplified within its own microreactor, excluding competing or contaminating sequences. Amplification of the entire fragment collection is carried out in parallel; for each fragment, this produces several million copies of the original fragment per bead. Subsequently, the emulsions are broken to facilitate collection of the amplified fragments bound to their specific beads.

The clonally amplified fragments are enriched and loaded onto a PicoTiterPlate device for sequencing. The diameter of the PicoTiterPlate wells allows for only one bead per well. After addition of sequencing enzymes and reagents, the fluidics subsystem of the Genome Sequencer System serially flows nucleotides in a fixed order across the hundreds of thousands of wells containing one bead each. Addition of one (or more) nucleotide(s) complementary to the template strand results in a chemiluminescent signal recorded by the CCD camera of the Genome Sequencer System. The intensity of the resulting signal is proportional to the number of bases incorporated.

The combination of signal intensity and positional information generated across the PicoTiterPlate device allows the software to determine the sequence of 100,000 individual reads per 10-hour instrument run simultaneously.

Initially, investigators at the Smithsonian Conservation Biology Institute plan to use the GS Junior System’s DNA sequencing technology to gain deeper insight into the genetics of dangerous pathogens that threaten animal species.

“The power of next-generation sequencing is remarkable,” said Dr. Rob Fleischer, head of the Center for Conservation and Evolutionary Genetics. “We are thrilled to work with Roche to bring the GS Junior System into our laboratory. The system is perfectly sized for our research and the long read lengths are critical to our particular areas of focus in pathogen detection and viral/bacterial comparative genomics.”

“We are honored to support the Smithsonian Institution and the National Zoo’s animal conservation projects, which are vital to the future health of our planet,” said Dr. Thomas Schinecker, president of Roche’s 454 Life Sciences Company (Branford, CT, USA). “This collaboration demonstrates the tremendous potential of our sequencing technology to broaden understanding of all species on earth - from humans to plants and animals.”